error when running notebook from command line

[Alberto Arturo Vergani]

Dear experts,

I am trying to run a notebook from a command line on SpiNNaker server (JupyterLab interface).

I copyed in bottom the error I got.

In other systems, I dont have that error... do I have to install some extra libraries to have running it properly?

Thanks for the hint

Regards,

Alberto

[NbConvertApp] Converting notebook 2021-11-08_parameter-scanning.ipynb to notebook

Traceback (most recent call last):

  File "/usr/lib/python3.6/runpy.py", line 193, in _run_module_as_main

    "__main__", mod_spec)

  File "/usr/lib/python3.6/runpy.py", line 85, in _run_code

    exec(code, run_globals)

  File "/home/spinnaker/sPyNNaker/lib/python3.6/site-packages/ipykernel_launcher.py", line 15, in <module>

    from ipykernel import kernelapp as app

  File "/home/spinnaker/sPyNNaker/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 40, in <module>

    from .ipkernel import IPythonKernel

  File "/home/spinnaker/sPyNNaker/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 16, in <module>

    from .comm import CommManager

  File "/home/spinnaker/sPyNNaker/lib/python3.6/site-packages/ipykernel/comm/__init__.py", line 1, in <module>

    from .manager import *

  File "/home/spinnaker/sPyNNaker/lib/python3.6/site-packages/ipykernel/comm/manager.py", line 15, in <module>

    from .comm import Comm

  File "/home/spinnaker/sPyNNaker/lib/python3.6/site-packages/ipykernel/comm/comm.py", line 9, in <module>

    from ipykernel.kernelbase import Kernel

  File "/home/spinnaker/sPyNNaker/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 26, in <module>

    from tornado.queues import PriorityQueue, QueueEmpty

  File "/home/spinnaker/sPyNNaker/lib/python3.6/site-packages/tornado/queues.py", line 33, in <module>

    from tornado.concurrent import Future, future_set_result_unless_cancelled

ImportError: cannot import name 'future_set_result_unless_cancelled'

Traceback (most recent call last):

  File "/usr/local/bin/jupyter-nbconvert", line 8, in <module>

    sys.exit(main())

  File "/usr/local/lib/python2.7/dist-packages/jupyter_core/application.py", line 270, in launch_instance

    return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)

  File "/usr/local/lib/python2.7/dist-packages/traitlets/config/application.py", line 664, in launch_instance

    app.start()

  File "/usr/local/lib/python2.7/dist-packages/nbconvert/nbconvertapp.py", line 340, in start

    self.convert_notebooks()

  File "/usr/local/lib/python2.7/dist-packages/nbconvert/nbconvertapp.py", line 510, in convert_notebooks

    self.convert_single_notebook(notebook_filename)

  File "/usr/local/lib/python2.7/dist-packages/nbconvert/nbconvertapp.py", line 481, in convert_single_notebook

    output, resources = self.export_single_notebook(notebook_filename, resources, input_buffer=input_buffer)

  File "/usr/local/lib/python2.7/dist-packages/nbconvert/nbconvertapp.py", line 410, in export_single_notebook

    output, resources = self.exporter.from_filename(notebook_filename, resources=resources)

  File "/usr/local/lib/python2.7/dist-packages/nbconvert/exporters/exporter.py", line 179, in from_filename

    return self.from_file(f, resources=resources, **kw)

  File "/usr/local/lib/python2.7/dist-packages/nbconvert/exporters/exporter.py", line 197, in from_file

    return self.from_notebook_node(nbformat.read(file_stream, as_version=4), resources=resources, **kw)

  File "/usr/local/lib/python2.7/dist-packages/nbconvert/exporters/notebook.py", line 32, in from_notebook_node

    nb_copy, resources = super(NotebookExporter, self).from_notebook_node(nb, resources, **kw)

  File "/usr/local/lib/python2.7/dist-packages/nbconvert/exporters/exporter.py", line 139, in from_notebook_node

    nb_copy, resources = self._preprocess(nb_copy, resources)

  File "/usr/local/lib/python2.7/dist-packages/nbconvert/exporters/exporter.py", line 316, in _preprocess

    nbc, resc = preprocessor(nbc, resc)

  File "/usr/local/lib/python2.7/dist-packages/nbconvert/preprocessors/base.py", line 47, in __call__

    return self.preprocess(nb, resources)

  File "/usr/local/lib/python2.7/dist-packages/nbconvert/preprocessors/execute.py", line 403, in preprocess

    with self.setup_preprocessor(nb, resources, km=km):

  File "/usr/lib/python2.7/contextlib.py", line 17, in __enter__

    return self.gen.next()

  File "/usr/local/lib/python2.7/dist-packages/nbconvert/preprocessors/execute.py", line 345, in setup_preprocessor

    self.km, self.kc = self.start_new_kernel(**kwargs)

  File "/usr/local/lib/python2.7/dist-packages/nbconvert/preprocessors/execute.py", line 296, in start_new_kernel

    kc.wait_for_ready(timeout=self.startup_timeout)

  File "/usr/local/lib/python2.7/dist-packages/jupyter_client/blocking/client.py", line 120, in wait_for_ready

    raise RuntimeError('Kernel died before replying to kernel_info')

RuntimeError: Kernel died before replying to kernel_info

Makefile:6: recipe for target 'default' failed

make: *** [default] Error 1

spinnaker@ad9205e05509:~/brainArt$ 

spinnaker@ad9205e05509:~/brainArt$ jupyter nbconvert --execute 2021-11-08_parameter-scanning.ipynb 

[NbConvertApp] Converting notebook 2021-11-08_parameter-scanning.ipynb to html

Traceback (most recent call last):

  File "/usr/lib/python3.6/runpy.py", line 193, in _run_module_as_main

    "__main__", mod_spec)

  File "/usr/lib/python3.6/runpy.py", line 85, in _run_code

    exec(code, run_globals)

  File "/home/spinnaker/sPyNNaker/lib/python3.6/site-packages/ipykernel_launcher.py", line 15, in <module>

    from ipykernel import kernelapp as app

  File "/home/spinnaker/sPyNNaker/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 40, in <module>

    from .ipkernel import IPythonKernel

  File "/home/spinnaker/sPyNNaker/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 16, in <module>

    from .comm import CommManager

  File "/home/spinnaker/sPyNNaker/lib/python3.6/site-packages/ipykernel/comm/__init__.py", line 1, in <module>

    from .manager import *

  File "/home/spinnaker/sPyNNaker/lib/python3.6/site-packages/ipykernel/comm/manager.py", line 15, in <module>

    from .comm import Comm

  File "/home/spinnaker/sPyNNaker/lib/python3.6/site-packages/ipykernel/comm/comm.py", line 9, in <module>

    from ipykernel.kernelbase import Kernel

  File "/home/spinnaker/sPyNNaker/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 26, in <module>

    from tornado.queues import PriorityQueue, QueueEmpty

  File "/home/spinnaker/sPyNNaker/lib/python3.6/site-packages/tornado/queues.py", line 33, in <module>

    from tornado.concurrent import Future, future_set_result_unless_cancelled

ImportError: cannot import name 'future_set_result_unless_cancelled'

Traceback (most recent call last):

  File "/usr/local/bin/jupyter-nbconvert", line 8, in <module>

    sys.exit(main())

  File "/usr/local/lib/python2.7/dist-packages/jupyter_core/application.py", line 270, in launch_instance

    return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)

  File "/usr/local/lib/python2.7/dist-packages/traitlets/config/application.py", line 664, in launch_instance

    app.start()

  File "/usr/local/lib/python2.7/dist-packages/nbconvert/nbconvertapp.py", line 340, in start

    self.convert_notebooks()

  File "/usr/local/lib/python2.7/dist-packages/nbconvert/nbconvertapp.py", line 510, in convert_notebooks

    self.convert_single_notebook(notebook_filename)

  File "/usr/local/lib/python2.7/dist-packages/nbconvert/nbconvertapp.py", line 481, in convert_single_notebook

    output, resources = self.export_single_notebook(notebook_filename, resources, input_buffer=input_buffer)

  File "/usr/local/lib/python2.7/dist-packages/nbconvert/nbconvertapp.py", line 410, in export_single_notebook

    output, resources = self.exporter.from_filename(notebook_filename, resources=resources)

  File "/usr/local/lib/python2.7/dist-packages/nbconvert/exporters/exporter.py", line 179, in from_filename

    return self.from_file(f, resources=resources, **kw)

  File "/usr/local/lib/python2.7/dist-packages/nbconvert/exporters/exporter.py", line 197, in from_file

    return self.from_notebook_node(nbformat.read(file_stream, as_version=4), resources=resources, **kw)

  File "/usr/local/lib/python2.7/dist-packages/nbconvert/exporters/html.py", line 95, in from_notebook_node

    return super(HTMLExporter, self).from_notebook_node(nb, resources, **kw)

  File "/usr/local/lib/python2.7/dist-packages/nbconvert/exporters/templateexporter.py", line 307, in from_notebook_node

    nb_copy, resources = super(TemplateExporter, self).from_notebook_node(nb, resources, **kw)

  File "/usr/local/lib/python2.7/dist-packages/nbconvert/exporters/exporter.py", line 139, in from_notebook_node

    nb_copy, resources = self._preprocess(nb_copy, resources)

  File "/usr/local/lib/python2.7/dist-packages/nbconvert/exporters/exporter.py", line 316, in _preprocess

    nbc, resc = preprocessor(nbc, resc)

  File "/usr/local/lib/python2.7/dist-packages/nbconvert/preprocessors/base.py", line 47, in __call__

    return self.preprocess(nb, resources)

  File "/usr/local/lib/python2.7/dist-packages/nbconvert/preprocessors/execute.py", line 403, in preprocess

    with self.setup_preprocessor(nb, resources, km=km):

  File "/usr/lib/python2.7/contextlib.py", line 17, in __enter__

    return self.gen.next()

  File "/usr/local/lib/python2.7/dist-packages/nbconvert/preprocessors/execute.py", line 345, in setup_preprocessor

    self.km, self.kc = self.start_new_kernel(**kwargs)

  File "/usr/local/lib/python2.7/dist-packages/nbconvert/preprocessors/execute.py", line 296, in start_new_kernel

    kc.wait_for_ready(timeout=self.startup_timeout)

  File "/usr/local/lib/python2.7/dist-packages/jupyter_client/blocking/client.py", line 120, in wait_for_ready

    raise RuntimeError('Kernel died before replying to kernel_info')

RuntimeError: Kernel died before replying to kernel_info

[Andrew Gait]

Hi Alberto,

We suspect that command is not working because you're not inside a virtualenv and there appears to be some confusion between python versions going on as well.

When you run a notebook on SpiNNaker you're either using the "sPyNNaker" or "sPyNNakerGit" kernels, so we suggest that whichever of these you are using, you should go into the relevant virtualenv; to do that from the terminal you need to go into the relevant directory (e.g.)

cd sPyNNakerGit

and then activate the virtualenv

source bin/activate

If this has worked then you should see (sPyNNakerGit) at the beginning of the command line prompt.  Now, hopefully, your jupyter nbconvert command should work (if not, there may be libraries you need to install yourself, which you should be able to do using pip install).

(If you need to come out of the virtualenv for some reason, then the command "deactivate" is what you need to use).

Andy

----------------------------------------------------
Dr. Andrew Gait (he/him),

Research Software Engineer,

APT Group,
Department of Computer Science,
The University of Manchester,
Oxford Road, Manchester M13 9PL

email: andre...@manchester.ac.uk
web: http://personalpages.manchester.ac.uk/staff/Andrew.Gait/

I do not expect a reply to this email outside of normal working hours

---

From: spinnak...@googlegroups.com <spinnak...@googlegroups.com> on behalf of Alberto Arturo Vergani <verga...@gmail.com>
Sent: 08 November 2021 16:14
To: SpiNNaker Users Group <spinnak...@googlegroups.com>
Subject: [SpiNNaker Mailing List] error when running notebook from command line

 

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